EMBOSS: Project Meeting (Mon 8th January 2007)


EBI: Alan Bleasby, Jon Ison, Mahmut Uludag,
Apologies: Peter Rice, Shaun McGlinchey, Rodrigo Lopez

1. Minutes of the last meeting

Minutes of the meeting of 11th December 2006 are here.

2. Software Development

2.1 Applications

Alan has fixed a memory leak in parsing GenBank in dbxflat.

2.2 Jemboss

Tim has provided a patch to Jemboss that allows compilation with the recently released Java 6. Alan/ has put the patches on the ftp server. This has been a necessary prelude to writing the Jemboss chapters for the Installation and Admin book.

Alan has confirmed that Jemboss now works with the latest stable releases of Java (6), Axis (1.4) and Tomcat (5.5.20). The beta release of Tomcat 6 (6.0.2) fails with SSL errors; we await a stable Tomcat v6.

2.3 Other development

Mahmut has been looking at the wrapped document literal version of SOAPLAB from Peter Ernst. Mahmut has implemented a common sequence object type under this for EMBOSS rather than, as it stood, one object for each input. He has also fixed a PHYLIP problem on the server. He now has 165 test cases working. The WIKI pages have been updated. Also, he has installed the latest Taverna CVS under Eclipse.

3. Administration

No items

4. Documentation and Training

4.1 Books

Jon has now got master documents for all books/chapters/appendices under CVS. They contain some meta information, for example author data. They also contain entity references to the section documents.

4.2 Training

Jon will be giving an EMBOSS demonstration to campus postgraduates.

5. User queries and answers

No items

6. AOB

No items

7. Date Of Next Meeting

The next meeting is on Monday 22nd January.